Variant report

Variant	rs9609689
Chromosome Location	chr22:33433761-33433762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:32750950-32761732..22:33433588-33439708	Hela-S3	cervix:
2	22:32740683-32750950..22:33433588-33439708	K562	blood:
3	22:32920308-32927723..22:33433588-33439708	Hela-S3	cervix:
4	22:32578360-32590642..22:33433588-33439708	K562	blood:
5	22:32872511-32874561..22:33433588-33439708	Hela-S3	cervix:
6	22:33190123-33206921..22:33433588-33439708	K562	blood:

Variant related genes	Relation type
ENSG00000271093	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000128253	Chromatin interaction
ENSG00000100234	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000205853	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11089601	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12484058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894536	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2413161	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413162	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55851829	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998705	0.81[EUR][1000 genomes]
rs62234240	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291322	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292646	0.89[ASN][1000 genomes]
rs8138938	0.89[ASN][1000 genomes]
rs9607004	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607005	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607006	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607007	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs9609678	0.80[GIH][hapmap]
rs9609679	0.81[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs9609680	0.84[GIH][hapmap]
rs9609681	0.84[GIH][hapmap];0.82[JPT][hapmap]
rs9609683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609684	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609685	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609686	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609688	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609690	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609691	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609692	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609693	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609695	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609696	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9609689	SEC14L3	cis	cerebellum	SCAN
rs9609689	RFPL1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33415000-33434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:33431000-33434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:33431000-33435200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:33431800-33434000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:33431800-33434800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr22:33432000-33433800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr22:33432000-33434000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:33432000-33434200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr22:33432200-33434200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr22:33432400-33433800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:33432400-33434200	Weak transcription	Brain Anterior Caudate	brain
12	chr22:33432400-33449800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr22:33432600-33433800	Weak transcription	Brain Angular Gyrus	brain
14	chr22:33433000-33435400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr22:33433200-33434800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:33433400-33434600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr22:33433400-33434600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr22:33433400-33435200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr22:33433600-33434000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr22:33433600-33434000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:33433600-33434000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
22	chr22:33433600-33434800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr22:33433600-33435200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr22:33433600-33435200	Enhancers	Fetal Brain Male	brain

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